Imaging Intron Evolution

Abstract

Intron evolution may be readily imaged through the combined use of the "dot plot" function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate "Multiz" alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.

Keywords: BLAST dot plots; GHR; Multiz alignment and conservation tool; SLC25A21; intron evolution.

Figure 1

(A) Abscissa: Human SLC25A21 (490,793 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 7704. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (B) Abscissa: Human GHR (292,898 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 1840. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (C) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all the 130 SINE Alus (462,572 nucleotides). Number of matches: 3220 (compared with A). Note the seemingly perfect alignment along the diagonal from the lower left corner to the upper right corner. (D) A partial, magnified, view of panel (C), showing a 10 K per 10 K area from the lower left corner, magnified by 50×. The gaps correspond to the removed SINE Alus. (E) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all TEs (298,209 nucleotides). These additional TEs belong to different categories, and some of them are much larger than the SINE Alus. Number of matches: 505. Note that the gaps (due to TEs) along the diagonal from the lower left corner to the upper right corner are now more visible at low magnification.

Figure 1

(A) Abscissa: Human SLC25A21 (490,793 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 7704. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (B) Abscissa: Human GHR (292,898 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 1840. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (C) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all the 130 SINE Alus (462,572 nucleotides). Number of matches: 3220 (compared with A). Note the seemingly perfect alignment along the diagonal from the lower left corner to the upper right corner. (D) A partial, magnified, view of panel (C), showing a 10 K per 10 K area from the lower left corner, magnified by 50×. The gaps correspond to the removed SINE Alus. (E) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all TEs (298,209 nucleotides). These additional TEs belong to different categories, and some of them are much larger than the SINE Alus. Number of matches: 505. Note that the gaps (due to TEs) along the diagonal from the lower left corner to the upper right corner are now more visible at low magnification.

Figure 1

(A) Abscissa: Human SLC25A21 (490,793 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 7704. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (B) Abscissa: Human GHR (292,898 nucleotides; the sequence from start to stop codons after removal of exons). Ordinate: the same sequence as in the Abscissa. Number of matches: 1840. Note the perfect alignment along the diagonal from the lower left corner to the upper right corner and the large number of matches outside the diagonal. (C) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all the 130 SINE Alus (462,572 nucleotides). Number of matches: 3220 (compared with A). Note the seemingly perfect alignment along the diagonal from the lower left corner to the upper right corner. (D) A partial, magnified, view of panel (C), showing a 10 K per 10 K area from the lower left corner, magnified by 50×. The gaps correspond to the removed SINE Alus. (E) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Human SLC25A21 after removal of all TEs (298,209 nucleotides). These additional TEs belong to different categories, and some of them are much larger than the SINE Alus. Number of matches: 505. Note that the gaps (due to TEs) along the diagonal from the lower left corner to the upper right corner are now more visible at low magnification.

Figure 2

(A) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Mouse slc25a21 (444,514 nucleotides). Number of matches: 1660. Note the significant alignment of most matches along the diagonal from the lower left corner to the upper right corner. The matches which are outside the diagonal mostly correspond to human and mouse TEs similar in structure. (B) Abscissa: Human SLC25A21 after the removal of all TEs. (298,209 nucleotides). Ordinate: Mouse slc25a21 after the removal of all TEs. (296,350 nucleotides). Number of matches: 266.The plot demonstrates a good overall alignment between the two sequences, while the gaps (which are usually short) correspond to poorly conserved sections. Note also the absence of significant matches outside the diagonal. (C) Abscissa: Human GHR (292,898 nucleotides). Ordinate: Mouse GHR (136,305 nucleotides). Number of matches: 280. Note the significant alignment of most matches along the diagonal from human GHR nucleotide 140,000 to the upper right corner, indicating that human nucleotides 1 to 140,000 have no matches with the mouse sequence, while the rest of the human sequence and the whole mouse sequence are homologous. The matches that are outside the diagonal mostly correspond to TEs that are similar in human and mouse. (D) Abscissa: Human GHR (homologous section only) after the removal of all TEs (85,058 nucleotides; from 78,000 to163,058). Ordinate: Mouse GHR after the removal of all TEs (89,777 nucleotides). Number of matches: 27. The plot demonstrates a general overall alignment between the two sequences, but the gaps are numerous and wide, corresponding to poorly conserved sections.

Figure 2

(A) Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Mouse slc25a21 (444,514 nucleotides). Number of matches: 1660. Note the significant alignment of most matches along the diagonal from the lower left corner to the upper right corner. The matches which are outside the diagonal mostly correspond to human and mouse TEs similar in structure. (B) Abscissa: Human SLC25A21 after the removal of all TEs. (298,209 nucleotides). Ordinate: Mouse slc25a21 after the removal of all TEs. (296,350 nucleotides). Number of matches: 266.The plot demonstrates a good overall alignment between the two sequences, while the gaps (which are usually short) correspond to poorly conserved sections. Note also the absence of significant matches outside the diagonal. (C) Abscissa: Human GHR (292,898 nucleotides). Ordinate: Mouse GHR (136,305 nucleotides). Number of matches: 280. Note the significant alignment of most matches along the diagonal from human GHR nucleotide 140,000 to the upper right corner, indicating that human nucleotides 1 to 140,000 have no matches with the mouse sequence, while the rest of the human sequence and the whole mouse sequence are homologous. The matches that are outside the diagonal mostly correspond to TEs that are similar in human and mouse. (D) Abscissa: Human GHR (homologous section only) after the removal of all TEs (85,058 nucleotides; from 78,000 to163,058). Ordinate: Mouse GHR after the removal of all TEs (89,777 nucleotides). Number of matches: 27. The plot demonstrates a general overall alignment between the two sequences, but the gaps are numerous and wide, corresponding to poorly conserved sections.

Figure 3

(A) Abscissa: Human SLC25A21 after the removal of all TEs (298,209 nucleotides). Ordinate: Chicken slc25a21 after the removal of all the TEs (200,341 nucleotides). Number of matches: 32. Short but likely significant matching segments align almost exactly along the diagonal from the lower left corner to the upper right corner. Gaps between matching segments are relatively wide and correspond to segments that do not share significant homologies. Chicken nucleotides aligning with human: 10,717 over 230,188, i.e., 4.66%. (B) A detail (magnification 5.7 times) of the lower left corner of (A) (52,000 by 32,000 nt).

Figure 3

(A) Abscissa: Human SLC25A21 after the removal of all TEs (298,209 nucleotides). Ordinate: Chicken slc25a21 after the removal of all the TEs (200,341 nucleotides). Number of matches: 32. Short but likely significant matching segments align almost exactly along the diagonal from the lower left corner to the upper right corner. Gaps between matching segments are relatively wide and correspond to segments that do not share significant homologies. Chicken nucleotides aligning with human: 10,717 over 230,188, i.e., 4.66%. (B) A detail (magnification 5.7 times) of the lower left corner of (A) (52,000 by 32,000 nt).

Figure 4

Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Zebrafish slc25a21 (200,517 nucleotides). The matching points significantly align along the diagonal from the lower left corner to the upper right corner. Aligned nucleotides = 1022 over 200,517, i.e., 0.51%.

Figure 5

Abscissa: Human SLC25A21 (490,793 nucleotides). Ordinate: Xenopus slc25a21 (187,108 nucleotides). The matching points do not correspond to TEs and significantly align along the diagonal from the lower left corner to the upper right corner. Aligned nucleotides = 846 over 187,108, i.e., 0.45%.

Figure 6

(A) An example of the analysis of conservation with the UCSC Genome Browser. The data, plotted as a bar graph, derive from the multialignment of 100 representative vertebrates. Each bar measures the average conservation/mutation of a series of 800 nucleotides; the blue bars (positive values) measure the conservation; the red bars (negative values) measure the mutation; the zero level is the conservation expected under neutral drift on the left of the scale (from −1.8647 to 2.20568). (B) SLC25A21: bar graph of the conservation profile in vertebrates. Each of the (minute) bars corresponds to 800 nucleotides. The series of arrows (top of the figure) indicate the direction of translation. The small vertical lines on the line of arrows mark the position of the exons. Other captions are the same as those in (A). (C) GHR: bar graph of the conservation profile in vertebrates. The same scale and other captions are used in (B), but each bar corresponds to 480 nucleotides.

Figure 7

(A) A section of the SLC25A21 sequence: The general vertebrate conservation exhibits five distinct peaks, but the chicken sequence matches only two of them. This section approximately corresponds to nucleotides 36,731 K to 36,784 K in human (refers to genomic sequences; Table 2). (B) A section of the SLC25A21 sequence: the general vertebrate conservation exhibits a long series of conserved nucleotides, while the chicken matches only a small part of the series and zebrafish exhibits no signal at all. This section approximately corresponds in human to nucleotides 36,792 K to 36,845 K.